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20 protocols using las image analysis software

1

Stomatal Characterization in Leaf Samples

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Pretreatment of samples was performed based on the method of Li, Tang & Xu (2013) (link). Fully expanded leaves were chosen from each plantlet to observe the stomata. The abaxial and adaxial surfaces of the leaves were wiped with wet absorbent cotton fiber. Then, transparent nail polish was smeared on the two sides of the leaves. After the nail polish had air-dried and formed a membrane, transparent adhesive tape was pressed onto each leaf and was subsequently stripped off. The transparent adhesive tape was then pressed on a slide, which was treated with a neutral plastic seal and made into a temporary slide. The slides were imaged using a Leica DMI 3000B microscope (Leica Microsystems, Wetzlar, Germany). The length, width, and density of stomata were measured with Leica LAS Image Analysis software (Leica Microsystems, Wetzlar, Germany). Stomatal area = Length × Width × 3.14 × 1/4 (μm2). Stomatal density = Number/Field/Field area.
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2

Pronotum Length Measurement in G. texensis

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Immediately prior to being placed in a trial, males were weighed on a Denver Instruments TP-64 digital balance (to the nearest 0.01 g) and the pronotum length measured using a stereoscope equipped with Leica LAS image analysis software (Leica Microsystems Inc., Buffalo Grove, IL, USA). Pronotum length (the distance from the anterior to posterior edges of the pronotum at the midline) is an excellent proxy for body size inG. texensis (Kelly, Tawes & Worthington, 2014 (link)).
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3

Immortalized Bone Marrow Cells

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After plating, bone marrow cells were grown to confluence and coinfected with HPV16 E6/E7 and hTERT lentiviral vectors (infection number 1). After a week the cells were split and infected again only with hTERT (infection number 2) and cultured until stabilization. Samples were observed and photographed with DMI 6000 inverted microscope (Leica Microsystems) using Leica LAS Image Analysis software (Leica Microsystems). The protocol was also reported in Miceli et al. [27 (link)].
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4

Visualizing Nodulation Dynamics in Composite Plants

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Composite plants transformed with the pMtARF3:GFP-GUS or pMtARF4a:GFP-GUS were transferred to square petri dishes (12 cm × 12 cm) containing slanted agar-Fahraeus medium. GFP fluorescence of roots was visualized with an inverted microscope (Olympus IX51) using UV light with appropriate filters for GFP. For detection of GFP and RFP fluorescence in S. meliloti inoculated roots and in nodules, confocal microscopy was performed at 5 and 9 dpi with an S. meliloti strain expressing RFP (Tian et al., 2012 (link)) using an inverted SP5 confocal microscope (Leica Microsystems). GFP and RFP were excited using 488- and 543-nm lasers, and emissions were collected from 498 to 552 nm and from 578 to 626 nm, respectively. Images were processed with the LAS Image Analysis software (Leica Microsystems).
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5

Quantifying Liver Fibrosis via Immunohistochemistry

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A Leica DM microscope was used to acquire images of the sections. Portal tracts were randomly chosen in the liver, five from each slide in ×20/×40 magnification. The proportion of antibody positive area (area percent) was calculated for α-SMA with LAS Image Analysis software (Leica Microsystem). Slides were graded into three groups according to the area percent values. Grade I (mild) 0–4, Grade II (moderate) 5–9 and Grade III (severe) >10 [Figures 13]. The pathologist was blinded to the clinical outcome.
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6

Microscopic Analysis of Plant Nodules

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Nodule tissue was processed as described in Zanetti et al. 2010 . Sections of 1-2 μm were stained with 0.04% toluidine blue and examined with an Olympus IX51 inverted microscope (OLYMPUS CORPORATION). Ultrathin sections of 70 nm were stained with uranyl acetate and lead citrate, and analyzed with a JEM 1200 EX II (JEOL, Tokio, Japan) transmission electron microscope. Confocal microscopy for subcellular localization analysis and observation of ITs were performed on N. benthamiana leaves or root segments of wild type and transgenic roots of common bean with an inverted SP5 microscope (LEICA MICROSYS-TEMS, Wetzlar, Germany) using a ×20 or a ×63 objective (numerical aperture of 0.5). GFP, RFP, mCherry and DsRed were excited using 488 nm (GFP) and 543 nm (RFP, mCherry and DsRed) lasers and emissions were collected between 500 and 550 nm (GFP), 600-660 nm (RFP), 584-660 nm (mCherry) and 578-626 nm (DsRed). Images were processed with the LAS Image Analysis software (LEICA MICROSYSTEMS).
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7

Mitotic Spindle Morphology Assay

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HCT116 cells were grown on glass coverslips. After overnight incubation, the cells were treated with each individual compound for 16 h. The cells were fixed with 4% paraformaldehyde in phosphate-buffered saline for 20 min, and permeabilized with 0.2% Triton X-100 for 10 min at room temperature. The cells were then incubated with anti-α-tubulin-FITC antibody (Sigma) for 45 min, and nuclei were stained with NucRed647 for 10 min. The cells were then examined by a laser-scan confocal microscope (Leica DMI 4000 B). All images were captured with an HCX PL Apo 63x oil immersion objective. Images were processed and analyzed using Leica's LAS Image Analysis software. The percentage of mitotic cells with monopolar spindles was calculated out of a total number of a minimum of 20 mitotic cells per coverslip that were detected in different and randomly chosen microscopic fields.
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8

Quantifying F-actin and Morphology Changes in mDCs

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IL-10-treated mDCs were stained with rhodamine phalloidin (Invitrogen, USA) and their F-actin structures and morphologies were examined on a confocal laser scanning microscope (Leica, Germany). Images were acquired and the F-actin contents were quantified by measuring the mean fluorescent intensities in each group. The lengths and numbers of cell membrane protrusions were also measured using Leica LAS Image Analysis software [28 (link)]. At least twenty cells in each group were selected for analysis.
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9

Cardiac Histology and Morphometry

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Paraffin-embedded 4-μm left ventricular sections were stained with H&E and picrosirius red, as described before,33 (link) or GS lectin Biotinylated Griffonia Simplicifolia Lectin I (Burlingame, CA). Morphometric analyses were performed using a microscope (Leica DM2000; Leica, Wetzlar, Germany), camera (Leica DFC295 3Mpix CMOS color), and LAS Image Analysis software (Leica). Quantifications of fibrosis via via picrosirius red staining and of cardiomyocyte area via laminin staining were performed as previously described.8 (link) Capillary density was analyzed in 8 lectin-stained sections/mouse at 40× magnification. Sections were analyzed with a capillary density assessment macro in ImageJ, from which tissue area (mm2), number of vessels, and number of vessels/mm2 were calculated.
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10

Immunohistochemical Staining Protocols

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Immunohistochemical fixation and staining protocols for FAH and H&E were completed as described (47 (link)). For analysis of turboGFO (tGFP), methods for FAH staining were used except the primary antibody was rabbit anti-tGFP (Axxora) used at 1:500 overnight at 4 °C. Fixation and staining methods for hF9 immunohistochemistry were as described (30 (link)).
For serial sections the primary antibodies used were in order: glutamine synthetase (1:200), Ki67 (1:200), Cyp2E1 (1:100, Abcam ab28146), Hnf4α (1:150, Santa Cruz Bio sc-8987) and hFIX (1:400). Vector IMPress conjugated to HRP detection kit was used as the secondary antibody. Positive staining was visualized with AEC (3-amino-9-ethylcarbazole) and DAB (3,3-diaminobenzidine substrate. Microscopy was performed on a DM IL LED microscope (Leica) using Leica LAS Image Analysis Software.
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